AMBER Archive (2008)

Subject: AMBER: H atom names in Amber

From: David A. Case (
Date: Thu Apr 17 2008 - 10:16:19 CDT

On Thu, Apr 17, 2008, wrote:
> I have a pdb file of a protonated protein. When I load this molecule into
> xleap, it adds further H atoms

This is probably because the names of the H atoms in your pdb file
don't mactch those in the LEaP library. Amber uses the IUPAC and "new" PDB
naming scheme for hydrogens, but many older files still use different names.

You can use the protonate program with the "-k" option to rename your H-atoms.
Look carefully at the small subset of your protein to see what is going on,
and to see what the protonate program does.

...good luck...dac

The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to